Starting phenix.real_space_refine on Tue May 7 10:05:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgg_19132/05_2024/8rgg_19132.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgg_19132/05_2024/8rgg_19132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgg_19132/05_2024/8rgg_19132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgg_19132/05_2024/8rgg_19132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgg_19132/05_2024/8rgg_19132.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgg_19132/05_2024/8rgg_19132.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 4787 2.51 5 N 1401 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 430": "NH1" <-> "NH2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B ARG 540": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 578": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "D TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "D ARG 330": "NH1" <-> "NH2" Residue "D ARG 348": "NH1" <-> "NH2" Residue "D ARG 373": "NH1" <-> "NH2" Residue "D ARG 381": "NH1" <-> "NH2" Residue "D ARG 405": "NH1" <-> "NH2" Residue "D PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 442": "NH1" <-> "NH2" Residue "D ARG 447": "NH1" <-> "NH2" Residue "D ARG 522": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 7679 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2297 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 8, 'TRANS': 277} Chain breaks: 1 Chain: "C" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 277 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 52} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 77 Chain: "D" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3329 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 33, 'TRANS': 422} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "G" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 462 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "H" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 462 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "I" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 426 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 172 Chain: "J" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 426 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 172 Time building chain proxies: 4.82, per 1000 atoms: 0.63 Number of scatterers: 7679 At special positions: 0 Unit cell: (87.768, 114.264, 104.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1470 8.00 N 1401 7.00 C 4787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 41.6% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 424 through 430 removed outlier: 3.920A pdb=" N ARG B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 437 Processing helix chain 'B' and resid 437 through 463 Processing helix chain 'B' and resid 480 through 508 removed outlier: 4.053A pdb=" N SER B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 548 removed outlier: 3.826A pdb=" N ARG B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B 515 " --> pdb=" O PRO B 511 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP B 548 " --> pdb=" O SER B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 552 Processing helix chain 'B' and resid 576 through 593 removed outlier: 3.579A pdb=" N VAL B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 631 removed outlier: 3.629A pdb=" N LYS B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 612 " --> pdb=" O GLN B 608 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN B 613 " --> pdb=" O LYS B 609 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET B 631 " --> pdb=" O ILE B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 635 through 653 removed outlier: 4.638A pdb=" N MET B 639 " --> pdb=" O GLN B 635 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B 642 " --> pdb=" O MET B 638 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 645 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE B 646 " --> pdb=" O SER B 642 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 649 " --> pdb=" O ALA B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 693 removed outlier: 3.603A pdb=" N ARG B 684 " --> pdb=" O ASN B 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 585 removed outlier: 3.666A pdb=" N ASP C 584 " --> pdb=" O MET C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 611 Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.880A pdb=" N GLN D 102 " --> pdb=" O PRO D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 129 removed outlier: 3.832A pdb=" N LEU D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 160 removed outlier: 3.984A pdb=" N GLN D 160 " --> pdb=" O PRO D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 522 through 534 removed outlier: 4.316A pdb=" N VAL D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 13 Processing helix chain 'G' and resid 35 through 61 Processing helix chain 'H' and resid 4 through 13 Processing helix chain 'H' and resid 35 through 61 Processing helix chain 'I' and resid 14 through 32 Processing helix chain 'I' and resid 34 through 50 removed outlier: 3.661A pdb=" N ILE I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 32 Processing helix chain 'J' and resid 34 through 50 Processing sheet with id=AA1, first strand: chain 'B' and resid 562 through 564 Processing sheet with id=AA2, first strand: chain 'C' and resid 552 through 558 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 566 through 568 current: chain 'I' and resid 72 through 78 removed outlier: 6.705A pdb=" N HIS I 72 " --> pdb=" O LYS I 87 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS I 87 " --> pdb=" O HIS I 72 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 81 through 87 current: chain 'J' and resid 81 through 87 Processing sheet with id=AA3, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.683A pdb=" N THR D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 168 through 169 removed outlier: 3.784A pdb=" N PHE D 194 " --> pdb=" O TYR D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 224 through 225 removed outlier: 3.582A pdb=" N TRP D 256 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP D 246 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU D 254 " --> pdb=" O ASP D 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 269 through 276 removed outlier: 3.666A pdb=" N GLN D 271 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL D 289 " --> pdb=" O GLN D 271 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N PHE D 284 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY D 300 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 290 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D 295 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY D 311 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU D 297 " --> pdb=" O THR D 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 341 through 342 removed outlier: 6.543A pdb=" N LYS D 361 " --> pdb=" O GLN D 385 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 395 through 400 removed outlier: 3.848A pdb=" N GLY D 412 " --> pdb=" O HIS D 416 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N HIS D 416 " --> pdb=" O GLY D 412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 438 through 443 removed outlier: 3.818A pdb=" N ALA D 440 " --> pdb=" O ALA D 454 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA D 454 " --> pdb=" O ALA D 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.626A pdb=" N VAL G 22 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER G 32 " --> pdb=" O ILE G 20 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE G 20 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR G 67 " --> pdb=" O PRO G 82 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU G 66 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N SER H 73 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE G 68 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE H 71 " --> pdb=" O PHE G 68 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG G 70 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU H 69 " --> pdb=" O ARG G 70 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG G 72 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N THR H 67 " --> pdb=" O PRO H 82 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE H 91 " --> pdb=" O GLY H 19 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.68 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1934 1.33 - 1.46: 1337 1.46 - 1.58: 4483 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 7784 Sorted by residual: bond pdb=" CA PRO D 99 " pdb=" C PRO D 99 " ideal model delta sigma weight residual 1.517 1.545 -0.028 6.70e-03 2.23e+04 1.75e+01 bond pdb=" CA LEU D 221 " pdb=" CB LEU D 221 " ideal model delta sigma weight residual 1.528 1.564 -0.035 1.13e-02 7.83e+03 9.78e+00 bond pdb=" N GLY D 501 " pdb=" CA GLY D 501 " ideal model delta sigma weight residual 1.444 1.474 -0.030 1.02e-02 9.61e+03 8.76e+00 bond pdb=" CZ ARG D 348 " pdb=" NH2 ARG D 348 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.64e+00 bond pdb=" N PRO D 230 " pdb=" CD PRO D 230 " ideal model delta sigma weight residual 1.473 1.432 0.041 1.40e-02 5.10e+03 8.45e+00 ... (remaining 7779 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.43: 135 105.43 - 112.85: 3831 112.85 - 120.27: 3393 120.27 - 127.69: 3216 127.69 - 135.11: 62 Bond angle restraints: 10637 Sorted by residual: angle pdb=" CA PHE D 439 " pdb=" CB PHE D 439 " pdb=" CG PHE D 439 " ideal model delta sigma weight residual 113.80 120.71 -6.91 1.00e+00 1.00e+00 4.77e+01 angle pdb=" N ALA J 11 " pdb=" CA ALA J 11 " pdb=" C ALA J 11 " ideal model delta sigma weight residual 107.23 118.10 -10.87 1.67e+00 3.59e-01 4.23e+01 angle pdb=" C LEU D 255 " pdb=" N TRP D 256 " pdb=" CA TRP D 256 " ideal model delta sigma weight residual 121.40 130.50 -9.10 1.52e+00 4.33e-01 3.59e+01 angle pdb=" CA PHE B 646 " pdb=" CB PHE B 646 " pdb=" CG PHE B 646 " ideal model delta sigma weight residual 113.80 119.54 -5.74 1.00e+00 1.00e+00 3.30e+01 angle pdb=" C ARG D 206 " pdb=" N PRO D 207 " pdb=" CA PRO D 207 " ideal model delta sigma weight residual 119.24 125.16 -5.92 1.04e+00 9.25e-01 3.24e+01 ... (remaining 10632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 4362 17.04 - 34.08: 268 34.08 - 51.11: 30 51.11 - 68.15: 14 68.15 - 85.19: 9 Dihedral angle restraints: 4683 sinusoidal: 1328 harmonic: 3355 Sorted by residual: dihedral pdb=" CA VAL G 17 " pdb=" C VAL G 17 " pdb=" N GLN G 18 " pdb=" CA GLN G 18 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA LEU D 255 " pdb=" C LEU D 255 " pdb=" N TRP D 256 " pdb=" CA TRP D 256 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ALA J 11 " pdb=" C ALA J 11 " pdb=" N ASP J 12 " pdb=" CA ASP J 12 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 4680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 889 0.097 - 0.195: 344 0.195 - 0.292: 48 0.292 - 0.390: 5 0.390 - 0.487: 4 Chirality restraints: 1290 Sorted by residual: chirality pdb=" CA THR D 309 " pdb=" N THR D 309 " pdb=" C THR D 309 " pdb=" CB THR D 309 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CA THR G 25 " pdb=" N THR G 25 " pdb=" C THR G 25 " pdb=" CB THR G 25 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA SER D 239 " pdb=" N SER D 239 " pdb=" C SER D 239 " pdb=" CB SER D 239 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 ... (remaining 1287 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 169 " -0.134 2.00e-02 2.50e+03 7.20e-02 1.30e+02 pdb=" CG TRP D 169 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP D 169 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP D 169 " 0.083 2.00e-02 2.50e+03 pdb=" NE1 TRP D 169 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TRP D 169 " 0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP D 169 " 0.100 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 169 " -0.080 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 169 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP D 169 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 674 " 0.124 2.00e-02 2.50e+03 6.36e-02 8.09e+01 pdb=" CG TYR B 674 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR B 674 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR B 674 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR B 674 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR B 674 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR B 674 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 674 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 298 " -0.106 2.00e-02 2.50e+03 5.37e-02 7.20e+01 pdb=" CG TRP D 298 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP D 298 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP D 298 " 0.048 2.00e-02 2.50e+03 pdb=" NE1 TRP D 298 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP D 298 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 298 " 0.063 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 298 " -0.073 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 298 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP D 298 " -0.048 2.00e-02 2.50e+03 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 3607 3.00 - 3.48: 7741 3.48 - 3.95: 11763 3.95 - 4.43: 12276 4.43 - 4.90: 21375 Nonbonded interactions: 56762 Sorted by model distance: nonbonded pdb=" OG SER D 231 " pdb=" OD1 ASP D 246 " model vdw 2.531 2.440 nonbonded pdb=" OD1 ASP D 246 " pdb=" OG SER D 248 " model vdw 2.547 2.440 nonbonded pdb=" OG SER B 549 " pdb=" OE2 GLU B 556 " model vdw 2.548 2.440 nonbonded pdb=" OG SER B 642 " pdb=" OE1 GLU B 688 " model vdw 2.549 2.440 nonbonded pdb=" OD1 ASP D 263 " pdb=" OG SER D 377 " model vdw 2.569 2.440 ... (remaining 56757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.790 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.320 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4596 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.041 7784 Z= 0.819 Angle : 1.849 10.868 10637 Z= 1.270 Chirality : 0.099 0.487 1290 Planarity : 0.014 0.191 1422 Dihedral : 13.181 85.189 2489 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1138 helix: 0.44 (0.22), residues: 414 sheet: 0.59 (0.31), residues: 189 loop : -0.91 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.029 TRP D 169 HIS 0.016 0.005 HIS D 404 PHE 0.090 0.012 PHE D 350 TYR 0.124 0.014 TYR B 674 ARG 0.009 0.001 ARG B 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 577 ASP cc_start: 0.4181 (m-30) cc_final: 0.3816 (p0) REVERT: B 613 GLN cc_start: 0.7368 (mt0) cc_final: 0.6724 (mp10) REVERT: D 198 TRP cc_start: 0.6589 (m-90) cc_final: 0.6038 (m100) REVERT: D 374 MET cc_start: 0.2478 (mmm) cc_final: 0.1430 (mtp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2322 time to fit residues: 45.2675 Evaluate side-chains 74 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 HIS D 424 GLN ** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4902 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7784 Z= 0.265 Angle : 0.713 10.187 10637 Z= 0.392 Chirality : 0.047 0.235 1290 Planarity : 0.004 0.036 1422 Dihedral : 5.920 26.429 1195 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.42 % Allowed : 9.74 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.24), residues: 1138 helix: 1.72 (0.23), residues: 421 sheet: 0.10 (0.32), residues: 224 loop : -0.32 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 298 HIS 0.005 0.002 HIS D 418 PHE 0.026 0.003 PHE D 358 TYR 0.025 0.003 TYR B 674 ARG 0.006 0.001 ARG B 540 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 562 MET cc_start: 0.2769 (ptt) cc_final: 0.2405 (ptt) REVERT: B 577 ASP cc_start: 0.4603 (m-30) cc_final: 0.4116 (p0) REVERT: B 674 TYR cc_start: 0.3338 (t80) cc_final: 0.2689 (t80) REVERT: D 145 MET cc_start: 0.7392 (mmm) cc_final: 0.7031 (mmm) outliers start: 20 outliers final: 14 residues processed: 94 average time/residue: 0.2000 time to fit residues: 26.0133 Evaluate side-chains 77 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 534 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 451 PHE Chi-restraints excluded: chain D residue 507 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 534 GLN ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 HIS ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5239 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7784 Z= 0.342 Angle : 0.795 9.156 10637 Z= 0.434 Chirality : 0.048 0.143 1290 Planarity : 0.005 0.042 1422 Dihedral : 6.507 34.509 1195 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.89 % Favored : 94.02 % Rotamer: Outliers : 5.13 % Allowed : 11.79 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1138 helix: 0.92 (0.24), residues: 422 sheet: 0.03 (0.33), residues: 223 loop : -0.65 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 245 HIS 0.013 0.002 HIS B 574 PHE 0.027 0.004 PHE D 350 TYR 0.034 0.003 TYR D 486 ARG 0.015 0.001 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 61 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 577 ASP cc_start: 0.4531 (m-30) cc_final: 0.3861 (p0) REVERT: D 198 TRP cc_start: 0.6572 (m-90) cc_final: 0.6281 (m100) REVERT: D 241 GLU cc_start: 0.5773 (tp30) cc_final: 0.5476 (tp30) REVERT: D 256 TRP cc_start: 0.6706 (OUTLIER) cc_final: 0.6212 (m-10) REVERT: D 374 MET cc_start: 0.3236 (mmm) cc_final: 0.1585 (mtm) REVERT: D 386 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7923 (t80) outliers start: 30 outliers final: 19 residues processed: 83 average time/residue: 0.1814 time to fit residues: 22.2816 Evaluate side-chains 73 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 52 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 534 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 256 TRP Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 451 PHE Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 507 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 588 GLN ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5213 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7784 Z= 0.237 Angle : 0.666 11.803 10637 Z= 0.356 Chirality : 0.045 0.139 1290 Planarity : 0.004 0.037 1422 Dihedral : 5.896 30.853 1195 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.47 % Allowed : 12.82 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1138 helix: 1.28 (0.24), residues: 418 sheet: -0.28 (0.31), residues: 237 loop : -0.62 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 198 HIS 0.010 0.002 HIS D 280 PHE 0.023 0.002 PHE D 350 TYR 0.018 0.002 TYR B 674 ARG 0.002 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 56 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 577 ASP cc_start: 0.4568 (m-30) cc_final: 0.3822 (p0) REVERT: B 639 MET cc_start: 0.4805 (OUTLIER) cc_final: 0.4398 (tpp) REVERT: D 165 THR cc_start: 0.6273 (p) cc_final: 0.5940 (p) REVERT: D 198 TRP cc_start: 0.6575 (m-90) cc_final: 0.6116 (m100) REVERT: D 241 GLU cc_start: 0.5558 (tp30) cc_final: 0.4984 (tp30) REVERT: D 256 TRP cc_start: 0.6521 (OUTLIER) cc_final: 0.6105 (m-10) REVERT: D 374 MET cc_start: 0.3161 (mmm) cc_final: 0.1524 (mtm) REVERT: D 386 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7893 (t80) REVERT: D 439 PHE cc_start: 0.4012 (OUTLIER) cc_final: 0.3042 (p90) REVERT: D 463 PHE cc_start: 0.6587 (t80) cc_final: 0.6297 (t80) outliers start: 32 outliers final: 19 residues processed: 79 average time/residue: 0.1594 time to fit residues: 18.8789 Evaluate side-chains 73 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 50 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 534 GLN Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 256 TRP Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 451 PHE Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5287 moved from start: 0.6723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7784 Z= 0.255 Angle : 0.683 11.250 10637 Z= 0.365 Chirality : 0.045 0.133 1290 Planarity : 0.004 0.048 1422 Dihedral : 5.868 30.210 1195 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 6.15 % Allowed : 12.31 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1138 helix: 1.23 (0.24), residues: 419 sheet: -0.67 (0.31), residues: 244 loop : -0.72 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 245 HIS 0.005 0.001 HIS B 574 PHE 0.025 0.002 PHE D 350 TYR 0.021 0.002 TYR B 674 ARG 0.004 0.001 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 56 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 535 PHE cc_start: 0.4828 (OUTLIER) cc_final: 0.3365 (t80) REVERT: B 577 ASP cc_start: 0.4663 (m-30) cc_final: 0.4359 (p0) REVERT: D 198 TRP cc_start: 0.6533 (m-90) cc_final: 0.5937 (m100) REVERT: D 241 GLU cc_start: 0.5644 (tp30) cc_final: 0.5097 (tp30) REVERT: D 374 MET cc_start: 0.3040 (mmm) cc_final: 0.1809 (mtm) REVERT: D 386 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7921 (t80) REVERT: D 439 PHE cc_start: 0.4285 (OUTLIER) cc_final: 0.3289 (p90) REVERT: D 463 PHE cc_start: 0.6804 (t80) cc_final: 0.6503 (t80) outliers start: 36 outliers final: 23 residues processed: 84 average time/residue: 0.1750 time to fit residues: 21.6064 Evaluate side-chains 78 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 52 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 451 PHE Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 40.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 moved from start: 0.7200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7784 Z= 0.280 Angle : 0.710 12.268 10637 Z= 0.380 Chirality : 0.046 0.171 1290 Planarity : 0.005 0.036 1422 Dihedral : 6.029 30.634 1195 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 6.50 % Allowed : 13.85 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1138 helix: 1.12 (0.24), residues: 420 sheet: -0.85 (0.32), residues: 234 loop : -0.95 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 245 HIS 0.006 0.001 HIS B 574 PHE 0.026 0.002 PHE D 350 TYR 0.020 0.002 TYR B 674 ARG 0.005 0.001 ARG B 578 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 55 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: B 535 PHE cc_start: 0.4822 (OUTLIER) cc_final: 0.3526 (t80) REVERT: B 639 MET cc_start: 0.5498 (OUTLIER) cc_final: 0.5108 (tpp) REVERT: D 374 MET cc_start: 0.2843 (mmm) cc_final: 0.1494 (mtm) REVERT: D 386 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.8043 (t80) REVERT: D 439 PHE cc_start: 0.4930 (OUTLIER) cc_final: 0.3858 (p90) REVERT: D 463 PHE cc_start: 0.6873 (t80) cc_final: 0.6448 (t80) outliers start: 38 outliers final: 24 residues processed: 85 average time/residue: 0.1693 time to fit residues: 21.3098 Evaluate side-chains 78 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 50 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 534 GLN Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 451 PHE Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 79 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN B 689 ASN D 282 HIS ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5175 moved from start: 0.7120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7784 Z= 0.152 Angle : 0.597 13.141 10637 Z= 0.309 Chirality : 0.045 0.321 1290 Planarity : 0.004 0.037 1422 Dihedral : 5.107 27.411 1195 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.27 % Allowed : 15.56 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1138 helix: 2.11 (0.25), residues: 423 sheet: -0.62 (0.33), residues: 240 loop : -0.78 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 198 HIS 0.004 0.001 HIS B 622 PHE 0.020 0.002 PHE D 350 TYR 0.017 0.001 TYR B 575 ARG 0.005 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 68 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 535 PHE cc_start: 0.4477 (OUTLIER) cc_final: 0.3609 (t80) REVERT: B 639 MET cc_start: 0.5382 (OUTLIER) cc_final: 0.5163 (tpp) REVERT: D 198 TRP cc_start: 0.6482 (m-90) cc_final: 0.5823 (m100) REVERT: D 241 GLU cc_start: 0.5407 (tp30) cc_final: 0.5139 (tp30) REVERT: D 256 TRP cc_start: 0.6307 (OUTLIER) cc_final: 0.5977 (m-10) REVERT: D 439 PHE cc_start: 0.4599 (OUTLIER) cc_final: 0.3440 (p90) REVERT: D 463 PHE cc_start: 0.6471 (t80) cc_final: 0.6266 (t80) outliers start: 25 outliers final: 15 residues processed: 84 average time/residue: 0.1827 time to fit residues: 22.1635 Evaluate side-chains 71 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 52 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 256 TRP Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 451 PHE Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 507 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 605 ASN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5292 moved from start: 0.7501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7784 Z= 0.223 Angle : 0.650 11.715 10637 Z= 0.344 Chirality : 0.046 0.303 1290 Planarity : 0.004 0.039 1422 Dihedral : 5.333 27.253 1195 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.44 % Allowed : 16.75 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1138 helix: 1.91 (0.25), residues: 422 sheet: -0.64 (0.34), residues: 227 loop : -0.82 (0.31), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 245 HIS 0.005 0.001 HIS D 328 PHE 0.022 0.002 PHE D 350 TYR 0.038 0.002 TYR D 437 ARG 0.006 0.001 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 52 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 535 PHE cc_start: 0.4733 (OUTLIER) cc_final: 0.3672 (t80) REVERT: B 631 MET cc_start: 0.3748 (mpp) cc_final: 0.3228 (mpp) REVERT: D 198 TRP cc_start: 0.6459 (m-90) cc_final: 0.5796 (m100) REVERT: D 241 GLU cc_start: 0.5471 (tp30) cc_final: 0.5153 (tp30) REVERT: D 256 TRP cc_start: 0.6433 (OUTLIER) cc_final: 0.6062 (m-10) REVERT: D 386 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7891 (t80) REVERT: D 439 PHE cc_start: 0.4745 (OUTLIER) cc_final: 0.3611 (p90) REVERT: D 463 PHE cc_start: 0.6882 (t80) cc_final: 0.6478 (t80) outliers start: 26 outliers final: 20 residues processed: 70 average time/residue: 0.1584 time to fit residues: 16.8970 Evaluate side-chains 75 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 51 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 256 TRP Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 451 PHE Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 622 HIS ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5454 moved from start: 0.8242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7784 Z= 0.351 Angle : 0.800 11.598 10637 Z= 0.429 Chirality : 0.049 0.310 1290 Planarity : 0.005 0.047 1422 Dihedral : 6.343 30.123 1195 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.76 % Allowed : 17.78 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.26), residues: 1138 helix: 0.94 (0.25), residues: 424 sheet: -1.14 (0.34), residues: 219 loop : -1.13 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 245 HIS 0.008 0.002 HIS D 163 PHE 0.020 0.003 PHE D 350 TYR 0.046 0.003 TYR D 437 ARG 0.005 0.001 ARG D 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 49 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 535 PHE cc_start: 0.4649 (OUTLIER) cc_final: 0.3856 (t80) REVERT: D 241 GLU cc_start: 0.5780 (tp30) cc_final: 0.5548 (tp30) REVERT: D 386 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.8130 (t80) REVERT: D 439 PHE cc_start: 0.5063 (OUTLIER) cc_final: 0.4034 (p90) outliers start: 22 outliers final: 19 residues processed: 66 average time/residue: 0.1729 time to fit residues: 16.8684 Evaluate side-chains 69 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 47 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 451 PHE Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5289 moved from start: 0.8080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7784 Z= 0.176 Angle : 0.628 11.757 10637 Z= 0.326 Chirality : 0.045 0.281 1290 Planarity : 0.004 0.042 1422 Dihedral : 5.402 28.204 1195 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.59 % Allowed : 17.09 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1138 helix: 1.77 (0.25), residues: 422 sheet: -0.83 (0.34), residues: 223 loop : -0.96 (0.31), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 443 HIS 0.005 0.001 HIS B 622 PHE 0.017 0.002 PHE D 350 TYR 0.028 0.002 TYR D 437 ARG 0.003 0.000 ARG D 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 53 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 535 PHE cc_start: 0.4366 (OUTLIER) cc_final: 0.3593 (t80) REVERT: D 439 PHE cc_start: 0.4887 (OUTLIER) cc_final: 0.3666 (p90) REVERT: D 447 ARG cc_start: 0.6722 (mtp-110) cc_final: 0.6496 (ttt90) REVERT: D 463 PHE cc_start: 0.6727 (t80) cc_final: 0.6344 (t80) outliers start: 21 outliers final: 17 residues processed: 67 average time/residue: 0.1486 time to fit residues: 15.3383 Evaluate side-chains 71 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 52 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 451 PHE Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 78 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.103752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.092486 restraints weight = 40984.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.093195 restraints weight = 33693.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.093541 restraints weight = 30806.946| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.8169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7784 Z= 0.180 Angle : 0.612 12.469 10637 Z= 0.316 Chirality : 0.045 0.281 1290 Planarity : 0.004 0.041 1422 Dihedral : 5.138 25.737 1195 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.59 % Allowed : 17.61 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 1138 helix: 2.07 (0.25), residues: 423 sheet: -0.83 (0.35), residues: 224 loop : -0.88 (0.31), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 245 HIS 0.003 0.001 HIS D 163 PHE 0.015 0.002 PHE D 350 TYR 0.020 0.002 TYR D 437 ARG 0.003 0.000 ARG D 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1542.19 seconds wall clock time: 29 minutes 25.26 seconds (1765.26 seconds total)